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JAL-3675 release notes for JAL-3750 JAL-3751
[jalview.git] / src / jalview / ws /
2020-08-05 Jim ProcterMerge branch 'patch/JAL-3692enaEndpointFlatfile' into... tree | commitdiff
2020-08-05 gmungocJAL-3692 parse multiline feature qualifiers and escaped... tree | commitdiff
2020-08-05 Jim ProcterMerge branch 'merge/JAL-3628+JAL-3608+JAL-3609+JAL... tree | commitdiff
2020-08-03 gmungocJAL-3692 refactor/complete parsing, more unit test... tree | commitdiff
2020-08-03 gmungocJAL-3692 EMBL flatfile fetcher / parser (todo: CDS... tree | commitdiff
2020-07-27 gmungocJAL-2656 JAL-3615 check response headers to test for... tree | commitdiff
2020-07-27 gmungocJAL-3615 used gzip endpoints for Pfam and Rfam tree | commitdiff
2020-06-15 Ben SoaresJAL-3628 Changed other calls to renameTo to use BackupF... tree | commitdiff
2020-01-28 gmungocMerge branch 'feature/JAL-3121gffAttributeMap' into... tree | commitdiff
2019-11-01 Ben SoaresJAL-3474 removed all .cvsignore files stored in the... improvement/JAL-3474_lots_of_.cvsignore_files tree | commitdiff
2019-08-22 gmungocJAL-3121 round trip GFF attributes including map-valued... tree | commitdiff
2019-06-26 Jim ProcterJAL-3332 test to check for duplicate db sources and... tree | commitdiff
2019-06-24 Jim ProcterJAL-3330 dbreffetcher: record any feature display model... tree | commitdiff
2019-04-23 Jim ProcterMerge branch 'develop' into bug/JAL-3224_getdown_change... tree | commitdiff
2019-04-15 gmungocJAL-3193 no separatge EnsemblGenomes source in Sequence... tree | commitdiff
2019-03-21 Ben SoaresJAL-3130 Replaced deprecated Class.newInstance() with... tree | commitdiff
2019-03-20 Ben SoaresJAL-3130 Lots of deprecation fixes. See utils/deprecat... tree | commitdiff
2019-03-06 gmungocMerge branch 'tasks/JAL-3035_remove_dasobert_dependency... tree | commitdiff
2019-03-06 gmungocJAL-3035 more das bits removed tree | commitdiff
2019-03-04 gmungocMerge branch 'bug/JAL-3120restoreFeatureColour' into... tree | commitdiff
2019-01-17 Jim ProcterJAL-3116 clear out whitespace when materialising Sequen... tree | commitdiff
2019-01-16 Jim ProcterMerge branch 'features/pca_jaxb_datasetrefs_JAL-3171_JA... tree | commitdiff
2018-12-17 Jim ProcterMerge branch 'develop' into bug/JAL-2541cutRelocateFeatures tree | commitdiff
2018-12-06 Ben SoaresJAL-3130 incorporating feature/JAL-3063jaxbNoCastor... tree | commitdiff
2018-09-21 gmungocJAL-3120 preserve feature colour/mincolour/maxcolour... bug/JAL-3120restoreFeatureColour tree | commitdiff
2018-09-17 gmungocJAL-3116 unit tests adapted to EMBL over JAXB tree | commitdiff
2018-09-14 gmungocJAL-3116 parse EMBL XML with JAXB (todo: update unit... tree | commitdiff
2018-09-13 gmungocJAL-3116 Uniprot XML unmarshalled using JAXB not Castor tree | commitdiff
2018-09-11 Jim ProcterMerge branch 'develop' into releases/Release_2_11_Branch tree | commitdiff
2018-06-26 Jim ProcterJAL-3035 - jalview-das is no more ! tree | commitdiff
2018-06-07 gmungocJAL-2920 wrap description in <html/> if it includes... tree | commitdiff
2018-06-06 Jim ProcterJAL-2920 revised TODO for JAL-3025 bug/JAL-2920_uniprotvariantfeature tree | commitdiff
2018-06-06 Jim ProcterJAL-2920 don’t output variant/original sequence as... tree | commitdiff
2018-06-06 Jim ProcterJAL-1920 JAL-3017 use newline not <br/> in description... tree | commitdiff
2018-06-04 Jim ProcterJAL-3017 parse multiple variant elements for uniprot... tree | commitdiff
2018-05-21 gmungocJAL-2920 use HGVS notation for protein variant feature tree | commitdiff
2018-03-08 gmungocJAL-2885 tests updated for code changes tree | commitdiff
2018-02-27 Jim ProcterMerge branch 'feature/JAL-2759' into merge/JAL-2759_2104 tree | commitdiff
2018-02-23 Jim ProcterMerge branch 'features/JAL-2885UniprotHttps' into relea... tree | commitdiff
2018-02-23 Jim ProcterJAL-2885 xfam https features/JAL-2885UniprotHttps tree | commitdiff
2018-02-23 Jim ProcterJAL-2885 XFAM_DOMAIN->XFAM_BASEURL tree | commitdiff
2018-02-23 Jim ProcterJAL-2885 renamed base URL getter from getDomain.. tree | commitdiff
2018-02-13 Jim ProcterJAL-2780 JAL-2781 don’t create a mapping if sequence... tree | commitdiff
2018-02-13 Jim ProcterJAL-2780 JAL-2781 only create a mapping entry or write... tree | commitdiff
2018-02-13 Jim ProcterJAL-2781 JAL-2780 include sequence start number when... tree | commitdiff
2018-02-13 Jim ProcterJAL-2781 refactor ‘trim retrieved sequence’ preference... tree | commitdiff
2018-02-11 Jim ProcterJAL-2780 JAL-2781 use PDBe numbering to map between... tree | commitdiff
2018-02-11 Jim ProcterJAL-2781 mark aligned positions via StructureMapping... tree | commitdiff
2018-02-11 Jim ProcterJAL-2780 JAL-2781 include a Mapping object in Structure... tree | commitdiff
2018-02-11 Jim ProcterJAL-2780 JAL-2781 UNASSIGNED positions marked as Intege... tree | commitdiff
2018-02-09 Jim ProcterUse the “PDBe” or “PDB” numbering (starts from 1, corre... tree | commitdiff
2018-02-09 Jim ProcterJAL-2780 JAL-2781 should always ensure SIFTS mappings... tree | commitdiff
2018-01-19 kiramtJAL-2759 Moved propagateInsertions out of HiddenColumns tree | commitdiff
2018-01-16 gmungocJAL-2885 uniprot now https, uniprot/ensembl/pfam/xfam... tree | commitdiff
2017-11-22 gmungocJAL-2069 spike updated with latest (FeatureTypeSettings) tree | commitdiff
2017-11-16 Jim ProcterMerge branch 'develop' into bug/JAL-2541cutRelocateFeatures tree | commitdiff
2017-11-13 Jim ProcterMerge branch 'features/JAL-2758_shorteruniprot' into... tree | commitdiff
2017-11-13 Jim ProcterJAL-2758 remove configurable behaviour - Uniprot sequen... tree | commitdiff
2017-11-13 Jim ProcterJAL-2758 typo tree | commitdiff
2017-11-06 Jim ProcterMerge branch 'bug/JAL-2541cutRelocateFeatures' into... tree | commitdiff
2017-10-27 gmungocJAL-1793 spike branch updated to latest tree | commitdiff
2017-10-26 Jim ProcterMerge branch 'feature/JAL-2488finalize' into develop tree | commitdiff
2017-10-25 Jim ProcterMerge branch 'bug/JAL-2392_deadlockonpdbdisplay' into... tree | commitdiff
2017-10-25 Jim ProcterJAL-2790 provide a cancel button for JABAWS and AACon... tree | commitdiff
2017-10-24 gmungocJAL-2738 update spike branch with latest tree | commitdiff
2017-10-12 Jim ProcterJAL-2773 add new flag to paintAlignment(updateOverview... features/JAL-2773_dontalwaysrecolourstructureonrepaintofoverview tree | commitdiff
2017-10-06 Jim ProcterJAL-2758 flag and tests for omitting uniprot accession... features/JAL-2758_shorteruniprot tree | commitdiff
2017-10-03 gmungocJAL-2738 copy to spikes/mungo tree | commitdiff
2017-09-29 Jim ProcterJAL-2748 formatting tree | commitdiff
2017-09-29 Jim ProcterJAL-2745 JAL-2748 direct download of XML from uniprot.org tree | commitdiff
2017-09-29 Jim ProcterJAL-2748 formatting tree | commitdiff
2017-09-29 Jim ProcterJAL-2745 JAL-2748 direct download of XML from uniprot.org tree | commitdiff
2017-09-29 Jim ProcterRevert "JAL-2745 update SIFTS FTP URL to HTTPS" tree | commitdiff
2017-09-29 Jim ProcterRevert "JAL-2745 update SIFTS FTP URL to HTTPS" tree | commitdiff
2017-09-29 Jim ProcterJAL-2745 update SIFTS FTP URL to HTTPS tree | commitdiff
2017-09-29 Jim ProcterJAL-2745 update SIFTS FTP URL to HTTPS tree | commitdiff
2017-09-29 Jim ProcterJAL-2745 stderr rather than stdout for unexpected HTTP... tree | commitdiff
2017-09-29 Jim ProcterJAL-2745 stderr rather than stdout for unexpected HTTP... tree | commitdiff
2017-09-29 gmungocJAL-2745 update www.ebi.ac.uk to https tree | commitdiff
2017-09-28 gmungocJAL-2745 update www.ebi.ac.uk to https tree | commitdiff
2017-09-14 gmungocJAL-2541 revised cut with features (work in progress) tree | commitdiff
2017-09-03 Jim ProcterMerge branch 'documentation/JAL-2675_release2102b1... tree | commitdiff
2017-09-01 gmungocJAL-2488 remove finalize methods tree | commitdiff
2017-08-22 Jim ProcterJAL-1551 formatting tree | commitdiff
2017-08-22 Jim ProcterJAL-2681 canonicalise DB source before fetching to... tree | commitdiff
2017-08-22 Jim ProcterJAL-2681 formatting tree | commitdiff
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList tree | commitdiff
2017-08-16 Jim ProcterJAL-2418 source formatting tree | commitdiff
2017-08-14 Jim ProcterJAL-2335 choose appropriate alphabet for filtering... tree | commitdiff
2017-08-14 Jim ProcterJAL-2335 source formatting tree | commitdiff
2017-08-14 Jim ProcterJAL-2335 filterNonStandardResidues configurable for... tree | commitdiff
2017-08-14 Jim ProcterJAL-2663 flag and filter to exclude non-standard amino... tree | commitdiff
2017-08-14 Jim ProcterJAL-2663 source formatting tree | commitdiff
2017-08-10 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-08-09 Jim ProcterJAL-2426 Rfam download suffix tree | commitdiff
2017-08-09 Jim ProcterJAL-2426 JAL-1270 report Xfam download URL used if... tree | commitdiff
2017-08-09 Jim ProcterJAL-2425 raw stockholm download URLs tree | commitdiff
2017-08-09 Jim ProcterJAL-2425 remove overloaded getSequenceRecords method... tree | commitdiff
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the... tree | commitdiff
2017-06-09 gmungocJAL-2446 merged to spike branch tree | commitdiff
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